|
| Status |
Public on Dec 30, 2022 |
| Title |
S_M_6_R2 |
| Sample type |
RNA |
| |
|
| Source name |
Susceptibe, Mock, 6hpi, Replicate2
|
| Organism |
Vitis vinifera |
| Characteristics |
genotype: N20/020 from cross population Red Globe x Regal Seedless
tissue: Leaf
treatment: 6hpi with water
|
| Treatment protocol |
On the adaxial side of the leaves of the different grapevine genotypes, P. viticola sporangia suspension (1.8x104 sporangia/ml) was sprayed on. As a control of the in vivo assay, plants were sprayed with water (mock inoculation).
|
| Growth protocol |
Grapevine cuttings were harvested, cut in similar sizes (with 2 buds per cutting) and partially immersed in a 30°C water bath within a 4°C chamber for 2 months. The cuttings were transferred to square plastic pots with a mixture of seedling substrate and perlite (3:1 v/v). Afterwards, the cuttings were placed in a greenhouse for 2 months with natural light conditions at a temperature between 5°C and 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 0.1 g of leaves with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands).
|
| Label |
Cy3
|
| Label protocol |
Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1
|
| |
|
| Hybridization protocol |
Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C), using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)
|
| Description |
Gene Expression at 6hpi with water
|
| Data processing |
Array images were analyzed using Agilent Feature Extraction software version 10.7.1.1 (Agilent Technologies, Santa Clara, CA). Default parameters (Protocol name_GE1_107_Sep09_grid name_028416_D_F_20100513) were used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as non-uniform outliers were excluded. To improve the resolution of the analysis, for the outliers, R Sincell workpakage was applied to obtain gProcessed Signals. GeneSpring MultiOmics Analysis version 14.9 (Agilent Technologies, Santa Clara, CA) was used. Data was normalised through a percentile shift of 75%, baseline median of all samples and different types of filters (expression, flag, data file and error - coefficient of variance <20%).
|
| |
|
| Submission date |
Jun 16, 2022 |
| Last update date |
Dec 30, 2022 |
| Contact name |
Vanessa Azevedo |
| E-mail(s) |
vsazevedo@fc.ul.pt
|
| Organization name |
Biosystems & Integrative Sciences Institute
|
| Department |
Plant Biology Department
|
| Lab |
Grapevine Pathogen System Lab
|
| Street address |
Campo Grande
|
| City |
Lisbon |
| ZIP/Postal code |
1749-016 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL30912 |
| Series (1) |
| GSE206244 |
Transcriptomic and methylation analysis of susceptible and tolerant grape genotypes following P. viticola infection |
|
